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Fix for the broken build: 

do **not** attempt to annotate if UnifiedGenotyper is called from another walker! Why this didn't break the build earlier I have no idea.

Ultimately, there should be a better way of interfacing UG with another walker -- what if some other walker wants the annotations from UG? But since we're calling map directly -- and the annotations don't get returned directly from map -- this needs to be handled differently, while the map function should ultimately return the LOD score or quality under the GCM alone.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2066 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-11-18 05:56:31 +00:00
parent 9fb50e9bd9
commit 95f1be94c0
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -167,7 +167,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
Pair<List<Genotype>, GenotypeLocusData> call = gcm.calculateGenotype(tracker, ref, MQ0freeContext, priors);
// annotate the call, if possible
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked) {
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked && ! (VARIANTS_FILE == null && out == null) ) {
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}